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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424
author | galaxyp |
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date | Wed, 08 May 2019 14:06:07 -0400 |
parents | 58a3e6cb2598 |
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Project Details 1: PeptideShaker Version: 1.16.31 2: Date: Thu Oct 11 10:41:54 CEST 2018 3: Experiment: Galaxy_Experiment_2018101110411539247311 4: Sample: Sample_2018101110411539247311 5: Replicate Number: 1 6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet Database Search Parameters 1: Precursor Tolerance Unit: ppm 2: Precursor Ion m/z Tolerance: 100.0 3: Fragment Ion Tolerance Unit: Da 4: Fragment Ion m/z Tolerance: 0.5 5: Cleavage: Enzyme 6: Enzyme: Trypsin 7: Missed Cleavages: 2 8: Specificity: Specific 9: Database: input_database.fasta 10: Forward Ion: b 11: Rewind Ion: y 12: Fixed Modifications: Carbamidomethylation of C 13: Variable Modifications: Oxidation of M 14: Refinement Variable Modifications: Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C 15: Refinement Fixed Modifications: Input Filters 1: Minimal Peptide Length: 1 2: Maximal Peptide Length: 30 3: Precursor m/z Tolerance: 10.0 4: Precursor m/z Tolerance Unit: Yes 5: Unrecognized Modifications Discarded: Yes Validation Summary 1: Proteins: #Validated: 2.0 2: Proteins: Total Possible TP: 2.0 3: Proteins: FDR Limit [%]: 0.0 4: Proteins: FNR Limit [%]: 0.0 5: Proteins: Confidence Limit [%]: 100.0 6: Proteins: PEP Limit [%]: 0.0 7: Proteins: Confidence Accuracy [%]: 0.0 8: Peptides: #Validated: 16.0 9: Peptides: Total Possible TP: 16.0 10: Peptides: FDR Limit [%]: 0.0 11: Peptides: FNR Limit [%]: 0.0 12: Peptides: Confidence Limit [%]: 100.0 13: Peptides: PEP Limit [%]: 0.0 14: Peptides: Confidence Accuracy [%]: 0.0 15: PSMs: #Validated PSM: 42.0 16: PSMs: Total Possible TP: 42.0 17: PSMs: FDR Limit [%]: 0.0 18: PSMs: FNR Limit [%]: 0.0 19: PSMs: Confidence Limit [%]: 100.0 20: PSMs: PEP Limit [%]: 0.0 21: PSMs: Confidence Accuracy [%]: 0.0 PTM Scoring Settings 1: Probabilistic Score: PhosphoRS 2: Accounting for Neutral Losses: No 3: Threshold: 95.0 Spectrum Counting Parameters 1: Method: NSAF 2: Validated Matches Only: No Annotation Settings 1: Intensity Limit: 0.75 2: Automatic Annotation: Yes 3: Selected Ions: b, y 4: Neutral Losses: H2O, NH3, CH4OS 5: Neutral Losses Sequence Dependence: Yes 6: Fragment Ion m/z Tolerance: 0.5